bp, from info i have the problem isn't the back its sides unless you cut transom in half it wouldn't grow, the sides can bow out if you banana'd the hull, or the length of the boat could grow if you concaved the hull, the easy way to see this is measure from bow to stern, for concave, for banana'd when you put the cap down you would have wide sides and short bow to stern
if neither of these exist i would check for obstructions . and 1/4 inch is nothing i had 1 cap had a half inch gap in rear of transom , however they were same year caps just made in different plants so i adjusted for 1/4 inch gap at bow and at stern and screwed it together and sealed it up.